29 results on '"Yue Zou"'
Search Results
2. Specific and efficient binding of Xeroderma pigmentosum complementation group A to double-strand/single-strand DNA junctions with 3' -and/or 5'-ssDNA branches
- Author
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Yang, Zhengguan, Roginskaya, Marina, Colis, Laureen C., Basu, Ashis K., Shell, Steven M., Yiyong Liu, Musich, Phillip R., Harris, Thomas M., and Yue Zou
- Subjects
Xeroderma pigmentosum -- Research ,DNA damage -- Research ,DNA-ligand interactions -- Research ,Biological sciences ,Chemistry - Abstract
A potential novel function of xeroderma pigmentosum group( XPA) in nucleotide excision repair (NER) to stabilize the unwound DNA intermediate surrounding the lesion using a homogeneous form of XPA purified from baculovirus-infected calls is studied. It is proposed that XPA plays a significant role in stabilizing, via its high affinity to ds-ssDNA junctions, the DNA strand opening surrounding the lesion for stable formation of preincision NER intermediates.
- Published
- 2006
3. Spectroscopic and theoretical insights into sequence effects of aminofluorene-induced conformational heterogeneity and nucleotide excision repair
- Author
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Meneni, Srinivasa Rao, Shell, Steven M., Gao, Lan, Jurecka, Petr, Wang Lee, Sponer, Jiri, Yue Zou, Chiarelli, M. Paul, and Bongsup P. Cho
- Subjects
Amino acids -- Structure ,Carcinogens -- Structure ,Cocarcinogens -- Structure ,DNA replication -- Analysis ,Nucleotide sequencing -- Analysis ,Quantum theory -- Analysis ,Biological sciences ,Chemistry - Abstract
The spectroscopic and computational studies about the effect of the base sequences on stacked (S) versus B-type (B) conformational heterogeneity caused by the major dG adduct derived from the model carcinogen 7-fluoro-2-aminofluorene (FAF) is reported. The findings show that FAF-modified DNA duplexes balanced between S and B conformations and interconverted slowly at room temperature.
- Published
- 2007
4. Structural characterization of human RPA sequential binding to single-stranded DNA using ssDNA as a molecular ruler
- Author
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Lifeng Cai, Roginskaya, Marina, Youxing Qu, Zhengguan Yang, Ying Xu, and Yue Zou
- Subjects
DNA-ligand interactions -- Structure ,Fluorescence spectroscopy -- Usage ,Proteins -- Analysis ,Biological sciences ,Chemistry - Abstract
The structural features of human replication protein A (RPA) interaction with single-stranded (ssDNA) are examined by using fluorescence spectroscopy. A global structure model is proposed for binding of the major RPA DNA binding domains (DBDs) to ssDNA.
- Published
- 2007
5. Recognition and incision of oxidative intrastrand cross-link lesions by UvrABC nuclease
- Author
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Chunang Gu, Qibin Zhang, Zhengguan Yang, Yuesong Wang, Yue Zou, and Yinsheng Wang
- Subjects
Escherichia coli -- Genetic aspects ,Enzymes -- Research ,Genetic research ,Biological sciences ,Chemistry - Abstract
Escherichia coli nucleotide excision repair (NER) enzymes UvrA, UvrB and UvrC were employed to examine the incision efficiency of duplex DNA carrying three different oxidative intrastrand cross-link lesions and tow dithymine photoproducts. The results showed that T[6-4]T was the best substrate for UvrA binding, followed by G[8-5]C, G[8-5m]mC and G[8-5m]T and then T[c,s]T and this suggests that oxidative intrastrand lesions might be substrates fro NER enzymes in vivo.
- Published
- 2006
6. Cooperative interaction of human XPA stabilizes and enhances specific binding of XPA to DNA damage
- Author
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Yu Liu, Yiyong Liu, Zhengguan Yang, Utzat, Christopher, Guizhi Wang, Basu, Ashis K., and Yue Zou
- Subjects
DNA damage -- Research ,Xeroderma pigmentosum -- Research ,Biological sciences ,Chemistry - Abstract
The oligomeric interactions of homogenous human xeroderma pigmentosum group A (XPA) protein with the 50-bp DNA substrate containing a single acetyl-2-aminofluorene (AAF)-DNA are characterized. The results suggest that the XPA dimer is probably the major form of the protein involved in the DNA damage recognition.
- Published
- 2005
7. DNA damage recognition of mutated forms of UrvB proteins in nucleotide excision repair
- Author
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Yue Zou, Huaxian Ma, Minko, Irina G., Shell, Steven M., Zhengguan Yang, Youxing Qu, and Ying Xu, G
- Subjects
Nucleotides -- Analysis ,Hydrophobic effect -- Analysis ,DNA repair -- Research ,Biological sciences ,Chemistry - Abstract
A single mutation of Y95W that enhances the binding of UvrB to structure-specific DNA adducts without the participation of UvrA, while mutations at other nearby aromatic and hydrophobic sites in the beta-hairpin did not exhibit any enhancement in binding are demonstrated. According to the results, the Y95 residue plays a unique role in stabilizing the interaction of UvrB with DNA damage by hydrophobic stacking.
- Published
- 2004
8. Thermodynamic characterization of the interaction of mutant UvrB protein with damaged DNA
- Author
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Huaxian Ma and Yue Zou
- Subjects
Nucleotides -- Analysis ,Fluorescence spectroscopy -- Analysis ,Mutation (Biology) -- Analysis ,DNA damage -- Research ,Biological sciences ,Chemistry - Abstract
The fluorescence spectroscopy is adopted to investigate the biochemical properties and thermodynamics of DNA damage recognition by the mutant protein. The binding of the UrvB (Y95W) mutant protein to a structure-specific 30 bp DNA substrate containing a single flurescein, which acts as both an adduct and a fluorophore, is examined.
- Published
- 2004
9. Spectroscopic and Theoretical Insights into Sequence Effects of Aminofluorene-Induced Conformational Heterogeneity and Nucleotide Excision Repair
- Author
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M. Paul Chiarelli, Wang Lee, Lan Gao, Steven M. Shell, Yue Zou, Srinivasarao Meneni, Jiri Sponer, Petr Jurečka, and Bongsup P. Cho
- Subjects
Circular dichroism ,education.field_of_study ,Magnetic Resonance Spectroscopy ,Base Sequence ,DNA Repair ,Chemistry ,Stereochemistry ,Base pair ,Circular Dichroism ,Population ,Temperature ,Nuclear magnetic resonance spectroscopy ,2-Acetylaminofluorene ,Models, Biological ,Biochemistry ,Adduct ,DNA Adducts ,Crystallography ,chemistry.chemical_compound ,Nucleic Acid Conformation ,Spectrophotometry, Ultraviolet ,education ,Conformational isomerism ,DNA ,Nucleotide excision repair - Abstract
A systematic spectroscopic and computational study was conducted in order to probe the influence of base sequences on stacked (S) versus B-type (B) conformational heterogeneity induced by the major dG adduct derived from the model carcinogen 7-fluoro-2-aminofluorene (FAF). We prepared and characterized eight 12-mer DNA duplexes (-AG*N- series, d[CTTCTAG*NCCTC]; -CG*N- series, d[CTTCTCG*NCCTC]), in which the central guanines (G*) were site-specifically modified with FAF with varying flanking bases (N = G, A, C, T). S/B heterogeneity was examined by CD, UV, and dynamic 19F NMR spectroscopy. All the modified duplexes studied followed a typical dynamic exchange between the S and B conformers in a sequence dependent manner. Specifically, purine bases at the 3'-flanking site promoted the S conformation (G > A > C > T). Simulation analysis showed that the S/B energy barriers were in the 14-16 kcal/mol range. The correlation times (tau = 1/kappa) were found to be in the millisecond range at 20 degrees C. The van der Waals energy force field calculations indicated the importance of the stacking interaction between the carcinogen and neighboring base pairs. Quantum mechanics calculations showed the existence of correlations between the total interaction energies (including electrostatic and solvation effects) and the S/B population ratios. The S/B equilibrium seems to modulate the efficiency of Escherichia coli UvrABC-based nucleotide excision repair in a conformation-specific manner: i.e., greater repair susceptibility for the S over B conformation and for the -AG*N- over the -CG*N- series. The results indicate a novel structure-function relationship, which provides insights into how bulky DNA adducts are accommodated by UvrABC proteins.
- Published
- 2007
10. Specific and Efficient Binding of Xeroderma Pigmentosum Complementation Group A to Double-Strand/Single-Strand DNA Junctions with 3‘- and/or 5‘-ssDNA Branches
- Author
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Thomas M. Harris, Constance M. Harris, Yiyong Liu, Laureen C. Colis, Yue Zou, Steven M. Shell, Ashis K. Basu, Zhengguan Yang, Phillip R. Musich, and Marina Roginskaya
- Subjects
endocrine system ,Xeroderma pigmentosum ,DNA Repair ,DNA repair ,DNA damage ,Molecular Sequence Data ,DNA, Single-Stranded ,Plasma protein binding ,Spodoptera ,Biology ,Biochemistry ,DNA-binding protein ,Article ,Cell Line ,DNA Adducts ,chemistry.chemical_compound ,medicine ,Animals ,Humans ,Replication protein A ,Base Sequence ,medicine.disease ,Molecular biology ,humanities ,Xeroderma Pigmentosum Group A Protein ,DNA-Binding Proteins ,enzymes and coenzymes (carbohydrates) ,chemistry ,Nucleic Acid Conformation ,Baculoviridae ,DNA ,DNA Damage ,Protein Binding ,Nucleotide excision repair - Abstract
Human XPA is an important DNA damage recognition protein in nucleotide excision repair (NER). We previously observed that XPA binds to the DNA lesion as a homodimer [Liu, Y., Liu, Y., Yang, Z., Utzat, C., Wang, G., Basu, A. K., and Zou, Y. (2005) Biochemistry 44, 7361-7368]. Herein we report that XPA recognized undamaged DNA double-strand/single-strand (ds-ssDNA) junctions containing ssDNA branches with binding affinity (Kd = 49.1 +/- 5.1 nM) much higher than its ability to bind to DNA damage. The recognized DNA junction structures include the Y-shape junction (with both 3'- and 5'-ssDNA branches), 3'-overhang junction (with a 3'-ssDNA branch), and 5'-overhang junction (with a 5'-ssDNA branch). Using gel filtration chromatography and gel mobility shift assays, we showed that the highly efficient binding appeared to be carried out by the XPA monomer and that the binding was largely independent of RPA. Furthermore, XPA efficiently bound to six-nucleotide mismatched DNA bubble substrates with or without DNA adducts including C8 guanine adducts of AF, AAF, and AP and the T[6,4]T photoproducts. Using a set of defined DNA substrates with varying degrees of DNA bending, we also found that the XPC-HR23B complex recognized DNA bending, whereas neither XPA nor the XPA-RPA complex could bind to bent DNA. We propose that, besides DNA damage recognition, XPA may also play a novel role in stabilizing, via its high affinity to ds-ssDNA junctions, the DNA strand opening surrounding the lesion for stable formation of preincision NER intermediates. Our results provide a plausible mechanistic interpretation for the indispensable requirement of XPA for both global genome and transcription-coupled repairs. Since ds-ssDNA junctions are common intermediates in many DNA metabolic pathways, the additional potential role of XPA in cellular processes is discussed.
- Published
- 2006
11. Recognition and Incision of Oxidative Intrastrand Cross-Link Lesions by UvrABC Nuclease
- Author
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Qibin Zhang, Yue Zou, Yinsheng Wang, Yuesong Wang, Chunang Gu, and Zhengguan Yang
- Subjects
Pyrimidine ,Molecular Sequence Data ,Pyrimidine dimer ,medicine.disease_cause ,Biochemistry ,Article ,Substrate Specificity ,chemistry.chemical_compound ,Escherichia coli ,medicine ,Pyrimidone ,Endodeoxyribonucleases ,Base Sequence ,Molecular Structure ,biology ,Escherichia coli Proteins ,DNA ,Molecular biology ,chemistry ,Pyrimidine Dimers ,Duplex (building) ,biology.protein ,Nucleic Acid Conformation ,Oxidation-Reduction ,Nucleotide excision repair - Abstract
Nucleotide excision repair (NER) is a repair pathway that removes a variety of bulky DNA lesions in both prokaryotic and eukaryotic cells. The perturbation of DNA helix structure caused by the oxidative intrastrand lesions could render them good substrates for the NER pathway. Here we employed Escherichia coli (E. coli) NER enzymes, i.e., UvrA, UvrB and UvrC, to examine the incision efficiency of duplex DNA carrying three different oxidative intrastrand cross-link lesions, that is, G[8-5]C, G[8-5m]mC, and G[8-5m]T, and two dithymine photoproducts, namely, the cis,syn-cyclobutane pyrimidine dimer (T[c,s]T) and pyrimidine(6-4)pyrimidone product (T[6-4]T). Our results showed that T[6-4]T was the best substrate for UvrA binding, followed by G[8-5]C, G [8-5m]mC and G[8-5m]T, and then by T[c,s]T. The efficiencies of the UvrABC incisions of these lesions were consistent with their UvrA binding affinities: The stronger the binding to UvrA, the higher the incision rate. In addition, flanking DNA sequences appeared to have little effect on the binding affinity of UvrA toward G[8-5]C as AG[8-5]CA was only slightly preferred over CG[8-5] CG. Consistently, these two sequences exhibited almost no difference in incision rates. Furthermore, we investigated the thermal stability of dodecameric duplexes containing a G[8-5m]mC or G[8-5m] T and our results revealed that these two lesions destabilized the duplex, due to an increase in free energy for duplex formation at 37°C, by approximately 5.4 kcal/mol and 3.6 kcal/mol, respectively. The destabilizations to DNA helix caused by those lesions, for the most part, are correlated with the binding affinities of UvrA and incision rates of UvrABC. Taken together, the results from this study suggest that oxidative intrastrand lesions might be substrates for NER enzymes in vivo.
- Published
- 2006
12. Mass Spectrometric Identification of Lysines Involved in the Interaction of Human Replication Protein A with Single-Stranded DNA
- Author
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Mamuka Kvaratskhelia, Yue Zou, Steven M. Shell, and Sonja Hess
- Subjects
HMG-box ,DNA damage ,Molecular Sequence Data ,DNA, Single-Stranded ,complex mixtures ,Biochemistry ,DNA-binding protein ,Article ,Mass Spectrometry ,Single-stranded binding protein ,chemistry.chemical_compound ,Replication Protein A ,Humans ,Amino Acid Sequence ,Replication protein A ,Sequence Homology, Amino Acid ,biology ,Protein footprinting ,Lysine ,Binding protein ,DNA-Binding Proteins ,enzymes and coenzymes (carbohydrates) ,chemistry ,biology.protein ,Electrophoresis, Polyacrylamide Gel ,DNA ,Protein Binding - Abstract
Human replication protein A (hRPA), a heterotrimeric single-stranded DNA (ssDNA) binding protein, is required for many cellular pathways including DNA damage repair, recombination, and replication as well as the ATR-mediated DNA damage response. While extensive effort has been devoted to understanding the structural relationships between RPA and ssDNA, information is currently limited to the RPA domains, the trimerization core, and a partial cocrystal structure. In this work, we employed a mass spectrometric protein footprinting method of single amino acid resolution to investigate the interactions of the entire heterotrimeric hRPA with ssDNA. In particular, we monitored surface accessibility of RPA lysines with NHS-biotin modification in the contexts of the free protein and the nucleoprotein complex. Our results not only indicated excellent agreement with the available crystal structure data for RPA70 DBD-AB-ssDNA complex but also revealed new protein contacts in the nucleoprotein complex. In addition to two residues, K263 and K343 of p70, previously identified by cocrystallography as direct DNA contacts, we observed protection of five additional lysines (K183, K259, K489, K577, and K588 of p70) upon ssDNA binding to RPA. Three residues, K489, K577, and K588, are located in ssDNA binding domain C and are likely to establish the direct contacts with cognate DNA. In contrast, no ssDNA-contacting lysines were identified in DBD-D. In addition, two lysines, K183 and K259, are positioned outside the putative ssDNA binding cleft. We propose that the protection of these lysines could result from the RPA interdomain structural reorganization induced by ssDNA binding.
- Published
- 2004
13. Effects of DNA Adduct Structure and Sequence Context on Strand Opening of Repair Intermediates and Incision by UvrABC Nuclease
- Author
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Ashis K. Basu, Christopher Utzat, Charlie Luo, Nicholas E. Geacintov, Zhengguan Yang, Yue Zou, and Steven M. Shell
- Subjects
chemistry.chemical_classification ,Endodeoxyribonucleases ,Base Sequence ,DNA Repair ,DNA repair ,Stereochemistry ,DNA damage ,Escherichia coli Proteins ,Molecular Sequence Data ,Electrophoretic Mobility Shift Assay ,Context (language use) ,Biochemistry ,Molecular biology ,Article ,Adduct ,DNA Adducts ,chemistry.chemical_compound ,chemistry ,DNA adduct ,Nucleotide ,DNA ,Nucleotide excision repair - Abstract
DNA damage recognition of nucleotide excision repair (NER) in Escherichia coli is achieved by at least two steps. In the first step, a helical distortion is recognized, which leads to a strand opening at the lesion site. The second step involves the recognition of the type of chemical modification in the single-stranded region of DNA during the processing of the lesions by UvrABC. In the current work, by comparing the efficiencies of UvrABC incision of several types of different DNA adducts, we show that the size and position of the strand opening are dependent on the type of DNA adducts. Optimal incision efficiency for the C8-guanine adducts of 2-aminofluorene (AF) and N-acetyl-2-aminofluorene (AAF) was observed in a bubble of three mismatched nucleotides, whereas the same for C8-guanine adduct of 1-nitropyrene and N(2)-guanine adducts of benzo[a]pyrene diol epoxide (BPDE) was noted in a bubble of six mismatched nucleotides. This suggests that the size of the aromatic ring system of the adduct might influence the extent and number of bases associated with the opened strand region catalyzed by UvrABC. We also showed that the incision efficiency of the AF or AAF adduct was affected by the neighboring DNA sequence context, which, in turn, was the result of differential binding of UvrA to the substrates. The sequence context effect on both incision and binding disappeared when a bubble structure of three bases was introduced at the adduct site. We therefore propose that these effects relate to the initial step of damage recognition of DNA structural distortion. The structure-function relationships in the recognition of the DNA lesions, based on our results, have been discussed.
- Published
- 2003
14. Dimerization of Human XPA and Formation of XPA2−RPA Protein Complex
- Author
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Leslie Y. Mao, Yue Zou, Yang Liu, Zheng guan Yang, and Jian-Ting Zhang
- Subjects
DNA Replication ,endocrine system ,DNA Repair ,Macromolecular Substances ,DNA repair ,DNA damage ,Dimer ,Plasma protein binding ,Spodoptera ,Biochemistry ,Article ,chemistry.chemical_compound ,Replication Protein A ,Escherichia coli ,Animals ,Humans ,Replication protein A ,Fluorocarbons ,Molecular mass ,Chemistry ,DNA replication ,Recombinant Proteins ,Xeroderma Pigmentosum Group A Protein ,DNA-Binding Proteins ,Molecular Weight ,Spectrometry, Fluorescence ,Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ,Chromatography, Gel ,Electrophoresis, Polyacrylamide Gel ,Caprylates ,Dimerization ,Protein Processing, Post-Translational ,Protein Binding ,Nucleotide excision repair - Abstract
XPA plays an important role in the DNA damage recognition during human nucleotide excision repair. Here we report that the XPA is a homodimer either in the free state or as a complex with human RPA in solution under normal conditions. The human XPA protein purified from baculovirus-infected sf21 insect cells has a molecular mass of 36 317 Da, as determined by mass spectroscopy. However, the apparent molecular mass of XPA determined by the native gel filtration chromatography was about 71 kDa, suggesting that XPA is a dimer. This observation was supported by a native PFO-PAGE and fluorescence spectroscopy analysis. XPA formed a dimer (XPA2) in a broad range of XPA and NaCl concentrations, and the dimerization was not due to the disulfide bond formation. Furthermore, a titration analysis of the binding of XPA to the human RPA indicated that it was the XPA2 that formed the complex with RPA. Finally, the difference between the mass spectrometric and the calculated masses of XPA implies that the protein contains posttranslational modifications. Taken together, our data suggest that the dimerization of XPA may play an important role in the DNA damage recognition of nucleotide excision repair.
- Published
- 2002
15. Intrastrand DNA Cross-Links as Tools for Studying DNA Replication and Repair: Two-, Three-, and Four-Carbon Tethers between the N2 Positions of Adjacent Guanines
- Author
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Yue Zou, Bennett Van Houten, Constance M. Harris, Thomas M. Harris, R. Stephen Lloyd, Agnieszka Kowalczyk, and J. Russ Carmical
- Subjects
DNA Replication ,inorganic chemicals ,Endodeoxyribonucleases ,Guanine ,Base Sequence ,DNA Repair ,Oligonucleotide ,Stereochemistry ,Escherichia coli Proteins ,Oligonucleotides ,DNA replication ,chemistry.chemical_element ,DNA-Directed DNA Polymerase ,Templates, Genetic ,Biochemistry ,DNA Adducts ,chemistry.chemical_compound ,Cross-Linking Reagents ,chemistry ,Nucleic Acid Conformation ,Carbon ,DNA - Abstract
A general protocol for preparation of oligonucleotides containing intrastrand cross-links between the exocyclic amino groups of adjacent deoxyguanosines has been developed. A series of 2, 3, and 4 methylene cross-links was incorporated site-specifically into an 11-mer (5'-GGCAGGTGGTG-3', cross-linked positions are underlined) via a reaction between oligonucleotide containing 2-fluoro-O(6)-trimethylsilylethyl deoxyinosines and the appropriate diamine (ethylenediamine, 1,3-diaminopropane, 1,4-diaminobutane). These cross-linked-oligonucleotides were studied for their ability to bend DNA by the method of Koo and Crothers [Koo, H. S., and Crothers, D. M. (1988) Proc. Natl. Acad. Sci. U.S.A. 85, 1763-1767] in which the mobility of ligated oligomers in nondenaturing polyacrylamide gels is evaluated. It was found that all cross-links induced bending (2-carbon cross-link, 30.0 +/- 4.0 deg/turn; 3-carbon cross-link, 11.7 +/- 1.6 deg/turn; 4-carbon cross-link, 7.4 +/- 1.0 deg/turn). Despite the differing extent of helical distortion exhibited by the cross-links, all appeared to be equally blocking to replication by the Escherichia coli polymerases, pol I, pol II, and pol III. In contrast, when incision of the cross-links by the E. coli UvrABC nucleotide incision complex was studied, the extent of incision of the cross-link was found to correlate closely with the degree of bending measured in the gel mobility assay, i.e., the efficiency of incision was 2-carbon3-carbon4-carbon.
- Published
- 2002
16. Effects of Geometric Isomerism and Ligand Substitution in Bifunctional Dinuclear Platinum Complexes on Binding Properties and Conformational Changes in DNA
- Author
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Yue Zou, Ana Paula Soares Fontes, K A Skov, Yun Qu, Philip K. Wu, Nicholas Farrell, T G Appleton, and John D. Roberts
- Subjects
inorganic chemicals ,Steric effects ,Coordination sphere ,Base Sequence ,Ligand ,Stereochemistry ,Molecular Sequence Data ,Platinum Compounds ,DNA ,Ligands ,Biochemistry ,chemistry.chemical_compound ,Isomerism ,chemistry ,Diamine ,parasitic diseases ,Pyridine ,Nucleic Acid Conformation ,Bifunctional ,Cis–trans isomerism ,Derivative (chemistry) ,Protein Binding - Abstract
The DNA binding profile of a series of dinuclear platinum complexes [{trans-PtCl-(L)2}2H2N(CH2)nNH2]2+ (L = NH3 or py; 1,1/t,t/NH3 and 1,1/t,t/py, respectively) and [{cis-PtCl-(NH3)2H2N(CH2)nNH2]2+ (1,1/c,c/NH3) was examined to compare the effects of geometrical isomerism and the presence of ligands other than NH3 in the coordination sphere. Steric effects, because of the geometry of the leaving groups cis to the diamine bridge or the presence of planar pyridine ligands, result in diminished binding to calf thymus DNA for these isomers. In contrast, the pyridine derivative shows a distinct binding preference for poly(dG-dC).poly(dG-dC) in comparison to both NH3 isomers. Both NH3 complexes induced the B-->Z transition in poly(dG-dC).poly(dG-dC), but the presence of a pyridine ligand stabilized the B conformation. The bifunctional binding of the NH3 isomers results in unwinding of supercoiled pUC19 plasmid DNA equivalent to cis-DDP, while the unwinding of the pyridine derivative is approximately twice that of the mononuclear trans-[PtCl2(py)2]. DNA-DNA interstrand cross-linking is very efficient for all three agents, but sequencing studies indicated that only the 1,1/t,t/NH3 derivative is capable of forming a (Pt,Pt) intrastrand cross-link to the adjacent guanines of a d(GpG) sequence. The effects on DNA caused by bifunctional binding of dinuclear complexes are compared with those from the mononuclear [PtCl2(NH3)2] isomers. The results are discussed with respect to the antitumor activity of the dinuclear series.
- Published
- 1995
17. Sequence Specificity of DNA-DNA Interstrand Cross-Link Formation by Cisplatin and Dinuclear Platinum Complexes
- Author
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Yue Zou, B. Van Houten, and Nicholas Farrell
- Subjects
Exonuclease ,Binding Sites ,Base Sequence ,Organoplatinum Compounds ,biology ,Stereochemistry ,Oligonucleotide ,Chemistry ,Base pair ,Molecular Sequence Data ,DNA ,Biochemistry ,DNA Adducts ,chemistry.chemical_compound ,Cross-Linking Reagents ,biology.protein ,A-DNA ,Cisplatin ,Primer (molecular biology) ,Binding site ,Polymerase - Abstract
The sequence specificity of interstrand cross-links induced in DNA by mononuclear and dinuclear platinum complexes in a 49-base-pair DNA duplex has been determined directly. This new assay takes advantage of the fact that 3'-->5' exonuclease digestion of randomly platinated DNA produces a pool of fragments of different lengths. This treatment allows identification of the spectrum of adducts impeding the exonuclease scission. Interstrand cross-linked adducts produce fragments that may remain complementary in the proximity of the binding site. As a result, these fragments may act as primer templates for extension upon subsequent treatment with a DNA polymerase. This extension increases the size of the oligonucleotide fragments, which may be evidenced by a more slowly migrating band on a sequencing gel. Concomitantly, the original band corresponding to the digested cross-link decreases in intensity. Therefore, comparison of a sequencing gel after digestion only and after the "digestion-extension" treatment should show the disappearance, or diminished band intensity, of only those fragments with interstrand cross-links. This approach was applied to the analysis of DNA interstrand cross-links formed by cis-[PtCl2(NH3)2] (cis-DDP) and [(trans-PtCl(NH3)2)2H2N(CH2)4NH2]Cl2. Cis-DDP was confirmed to form interstrand cross-links at d(GC) sequences but, interestingly, interstrand cross-links predominated in a sequence GCGG, with possible 1,3-intrastrand but no 1,2-intrastrand cross-links forming. The dinuclear compound formed 1,2, 1,3, and 1,4 DNA interstrand cross-links between guanines on opposite strands. In 1,3 and 1,4 cross-links, the guanines are separated by one and two base pairs, respectively, whereas a 1,2 cross-link is formed from guanines on neighboring base pairs.(ABSTRACT TRUNCATED AT 250 WORDS)
- Published
- 1994
18. (5'S)-8,5'-cyclo-2'-deoxyguanosine is a strong block to replication, a potent pol V-dependent mutagenic lesion, and is inefficiently repaired in Escherichia coli
- Author
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Benjamin Hilton, Rajat S. Das, Yue Zou, Ashis K. Basu, Vijay P. Jasti, and Savithri Weerasooriya
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DNA Replication ,congenital, hereditary, and neonatal diseases and abnormalities ,DNA Repair ,DNA polymerase ,DNA repair ,Biochemistry ,DNA polymerase delta ,Cockayne syndrome ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,medicine ,Escherichia coli ,Deoxyguanosine ,skin and connective tissue diseases ,SOS Response, Genetics ,030304 developmental biology ,0303 health sciences ,biology ,Rapid Report ,DNA replication ,nutritional and metabolic diseases ,Base excision repair ,DNA-Directed RNA Polymerases ,medicine.disease ,Molecular biology ,3. Good health ,chemistry ,Mutagenesis ,030220 oncology & carcinogenesis ,biology.protein ,Nucleotide excision repair - Abstract
8,5′-Cyclopurines, making up an important class of ionizing radiation-induced tandem DNA damage, are repaired only by nucleotide excision repair (NER). They accumulate in NER-impaired cells, as in Cockayne syndrome group B and certain Xeroderma Pigmentosum patients. A plasmid containing (5′S)-8,5′-cyclo-2′-deoxyguanosine (S-cdG) was replicated in Escherichia coli with specific DNA polymerase knockouts. Viability was S-cdA > S-cdG. In summary, S-cdG is a major block to DNA replication, highly mutagenic, and repaired slowly in E. coli.
- Published
- 2011
19. Structural characterization of human RPA sequential binding to single-stranded DNA using ssDNA as a molecular ruler
- Author
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Ying Xu, Zhengguan Yang, Yue Zou, Youxing Qu, Marina Roginskaya, and Lifeng Cai
- Subjects
Models, Molecular ,Mutation ,Binding Sites ,DNA, Single-Stranded ,Plasma protein binding ,Biology ,medicine.disease_cause ,Biochemistry ,Molecular biology ,Article ,Protein Structure, Tertiary ,enzymes and coenzymes (carbohydrates) ,chemistry.chemical_compound ,Spectrometry, Fluorescence ,chemistry ,Replication Protein A ,Biophysics ,medicine ,Humans ,Binding site ,Replication protein A ,DNA ,Protein Binding - Abstract
Human replication protein A (RPA), a heterotrimer composed of RPA70, RPA32, and RPA14 subunits, contains four single-stranded DNA (ssDNA) binding domains (DBD): DBD-A, DBD-B, and DBD-C in RPA70 and DBD-D in RPA32. Although crystallographic or NMR structures of these DBDs and a trimerization core have been determined, the structure of the full length of RPA or the RPA-ssDNA complex remains unknown. In this article, we have examined the structural features of RPA interaction with ssDNA by fluorescence spectroscopy. Using a set of oligonucleotides (dT) with varying lengths as a molecular ruler and also as the substrate, we have determined at single-nucleotide resolution the relative positions of the ssDNA with interacting intrinsic tryptophans of RPA. Our results revealed that Trp528 in DBD-C and Trp107 in DBD-D contact ssDNA at the 16th and 24th nucleotides (nt) from the 5'-end of the substrate, respectively. Evaluation of the relative spatial arrangement of RPA domains in the RPA-ssDNA complex suggested that DBD-B and DBD-C are spaced by about 4 nt ( approximately 19 A) apart, whereas DBD-C and DBD-D are spaced by about 7 nt ( approximately 34 A). On the basis of these geometric constraints, a global structure model for the binding of the major RPA DBDs to ssDNA was proposed.
- Published
- 2007
20. Thermodynamic characterization of the interaction of mutant UvrB protein with damaged DNA
- Author
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Yue Zou and Huaxian Ma
- Subjects
DNA Repair ,DNA damage ,DNA repair ,Mutant ,medicine.disease_cause ,Biochemistry ,Article ,Adduct ,chemistry.chemical_compound ,DNA Adducts ,Mutant protein ,medicine ,Mutation ,Acrylamide ,Chemistry ,Escherichia coli Proteins ,Osmolar Concentration ,DNA Helicases ,Temperature ,DNA ,Spectrometry, Fluorescence ,Models, Chemical ,Biophysics ,Mutagenesis, Site-Directed ,Thermodynamics ,Nucleotide excision repair ,DNA Damage ,Protein Binding - Abstract
During the DNA damage recognition of nucleotide excision repair in Escherichia coli the interaction of UvrB protein with damaged DNA ensures the recognition of differences in the intrinsic chemical structures of a variety of adduct molecules in DNA double helix. Our earlier study indicated that a single tyrosine-to-tryptophan mutation at residue 95 converted the UvrB to a protein [UvrB(Y95W)] that is able to bind to a structure-specific bubble DNA substrate, even in the absence of UvrA. Fluorescence spectroscopy therefore was adopted to investigate the biochemical properties and thermodynamics of DNA damage recognition by the mutant protein. We examined the binding of the UvrB(Y95W) mutant protein to a structure-specific 30 bp DNA substrate containing a single fluorescein which serves as both an adduct and a fluorophore. Binding of the protein to the substrate results in a significant reduction in fluorescence. By monitoring the fluorescence changes, binding isotherms were generated from a series of titration experiments at various physiological temperatures, and dissociation constants were determined. Analysis of our data indicate that interaction of UvrB(Y95W) protein with the adduct incurred a large negative change in heat capacity DeltaC(p)(o)(obs) (-1.1 kcal mol(-1) K(-1)), while the DeltaG(o)(obs) was relatively unchanged with temperature. Further study of the binding at various concentrations of KCl showed that on average only about 1.5 ion pairs were involved in formation of the UvrB-DNA complex. Together, these results suggested that hydrophobic interactions are the main driving forces for the recognition of DNA damage by UvrB protein.
- Published
- 2004
21. Hierarchy of DNA damage recognition in Escherichia coli nucleotide excision repair
- Author
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Charlie Luo, Nicholas E. Geacintov, and Yue Zou
- Subjects
DNA Repair ,DNA repair ,Base pair ,DNA polymerase ,DNA damage ,7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide ,Molecular Sequence Data ,Biochemistry ,Substrate Specificity ,DNA Adducts ,Adenosine Triphosphate ,Benzo(a)pyrene ,Escherichia coli ,Base Pairing ,chemistry.chemical_classification ,DNA ligase ,DNA clamp ,Endodeoxyribonucleases ,biology ,Base Sequence ,Escherichia coli Proteins ,Hydrolysis ,Deoxyguanosine ,Molecular biology ,chemistry ,biology.protein ,DNA mismatch repair ,Nucleotide excision repair ,DNA Damage ,Mutagens - Abstract
DNA damage recognition plays a central role in nucleotide excision repair (NER). Here we present evidence that in Escherichia coli NER, DNA damage is recognized through at least two separate but successive steps, with the first focused on distortions from the normal structure of the DNA double helix (initial recognition) and the second specifically recognizing the type of DNA base modifications (second recognition), after an initial local separation of the DNA strands. DNA substrates containing stereoisomeric (+)- or (-)-trans- or (+)- or (-)-cis-BPDE-N(2)-dG lesions in DNA duplexes of known conformations were incised by UvrABC nuclease with efficiencies varying by up to 3-fold. However, these stereoisomeric adducts, when positioned in an opened, single-stranded DNA region, were all incised with similar efficiencies and with enhanced rates (by factors of 1.4-6). These bubble substrates were also equally and efficiently incised by UvrBC nuclease without UvrA. Furthermore, removal of the Watson-Crick partner cytosine residue (leaving an abasic site) in the complementary strand opposite a (+)-cis-BPDE-N(2)-dG lesion led to a significant reduction in both the binding of UvrA and the incision efficiency of UvrABC by a factor of 5. These data suggest that E. coli NER features a dynamic two-stage recognition mechanism.
- Published
- 2001
22. Interaction of the UvrABC nuclease system with a DNA duplex containing a single stereoisomer of dG-(+)- or dG-(-)-anti-BPDE
- Author
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Bennett Van Houten, Nicholas E. Geacintov, Yue Zou, and Tongming Liu
- Subjects
Models, Molecular ,DNA Repair ,Stereochemistry ,Guanine ,Protein Conformation ,7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide ,Molecular Sequence Data ,Stereoisomerism ,Biochemistry ,Substrate Specificity ,chemistry.chemical_compound ,DNA Adducts ,Bacterial Proteins ,DNA adduct ,Escherichia coli ,A-DNA ,Adenosine Triphosphatases ,Binding Sites ,Endodeoxyribonucleases ,Base Sequence ,Chemistry ,Oligonucleotide ,Escherichia coli Proteins ,DNase-I Footprinting ,DNA Helicases ,Deoxyguanosine ,Hydrogen Bonding ,DNA ,DNA-Binding Proteins ,Kinetics ,Oligodeoxyribonucleotides ,Nucleic Acid Conformation ,Nucleotide excision repair ,Protein Binding - Abstract
Oligonucleotides containing site-specifically-modified N2-guanine (+)-trans-, (-)-trans-, (+)-cis-, and (-)-cis-BPDE adducts were ligated into 50-base-pair DNA fragments. These substrates were used in reactions with the Escherichia coli UvrABC nuclease system. The interaction of the UvrA2 and UvrA2B complexes with these four stereoisomers was probed using DNase I footprinting and gel mobility shift assays. DNase I digestion of substrates containing each stereoisomer of BPDE displayed a unique pattern which was consistent with the known structure of these DNA adducts. UvrA and UvrA2B appeared to interact very similarly with all four substrates. Binding of UvrA2 to these substrates produced a 33-bp footprint, and the UvrB--DNA complex resulted in footprint of 24 bp. The UvrABC nuclease system produced bimodal incisions at the eighth phosphate 5' and the fifth, sixth, or seventh phosphate 3' to the modified guanine. The variation of the 3' incision site was linked to the stereochemistry and orientation of the BPDE adduct. For example, the 3' incision of the 50-bp duplex containing (-)-trans-BPDE-N2-guanine was inhibited at the fifth phosphate. UvrABC nuclease incision kinetics revealed a hierarchy of specificity. The intercalative cis isomers were incised more efficiently than the corresponding trans isomers which lie in the minor groove. The (+) enantiomers were incised more efficiently than the (-) form for both cis and trans isomers. These observations reveal that UvrABC nuclease recognition and incision are directly influenced by the conformation of the DNA adduct.
- Published
- 1995
23. DNA Damage Recognition of Mutated Forms of UvrB Proteins in Nucleotide Excision Repair
- Author
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Nicholas E. Geacintov, Zhengguan Yang, Irina G. Minko, Youxing Qu, Steven M. Shell, R. Stephen Lloyd, Yue Zou, Ying Xu, and Huaxian Ma
- Subjects
Models, Molecular ,DNA Repair ,DNA repair ,DNA damage ,Molecular Sequence Data ,Biology ,Biochemistry ,Article ,DNA Glycosylases ,Substrate Specificity ,DNA Adducts ,chemistry.chemical_compound ,DNA Repair Protein ,Uracil-DNA Glycosidase ,Adenosine Triphosphatases ,Genetics ,Endodeoxyribonucleases ,Base Sequence ,Escherichia coli Proteins ,Mutagenesis ,DNA Helicases ,Tryptophan ,DNA-Binding Proteins ,Cross-Linking Reagents ,Spectrometry, Fluorescence ,Amino Acid Substitution ,chemistry ,Structural Homology, Protein ,DNA glycosylase ,Uracil-DNA glycosylase ,Mutagenesis, Site-Directed ,Tyrosine ,DNA ,DNA Damage ,Protein Binding ,Nucleotide excision repair - Abstract
The DNA repair protein UvrB plays an indispensable role in the stepwise and sequential damage recognition of nucleotide excision repair in Escherichia coli. Our previous studies suggested that UvrB is responsible for the chemical damage recognition only upon a strand opening mediated by UvrA. Difficulties were encountered in studying the direct interaction of UvrB with adducts due to the presence of UvrA. We report herein that a single point mutation of Y95W in which a tyrosine is replaced by a tryptophan results in an UvrB mutant that is capable of efficiently binding to structure-specific DNA adducts even in the absence of UvrA. This mutant is fully functional in the UvrABC incisions. The dissociation constant for the mutant-DNA adduct interaction was less than 100 nM at physiological temperatures as determined by fluorescence spectroscopy. In contrast, similar substitutions at other residues in the beta-hairpin with tryptophan or phenylalanine do not confer UvrB such binding ability. Homology modeling of the structure of E. coli UvrB shows that the aromatic ring of residue Y95 and only Y95 directly points into the DNA binding cleft. We have also examined UvrB recognition of both "normal" bulky BPDE-DNA and protein-cross-linked DNA (DPC) adducts and the roles of aromatic residues of the beta-hairpin in the recognition of these lesions. A mutation of Y92W resulted in an obvious decrease in the efficiency of UvrABC incisions of normal adducts, while the incision of the DPC adduct is dramatically increased. Our results suggest that Y92 may function differently with these two types of adducts, while the Y95 residue plays an unique role in stabilizing the interaction of UvrB with DNA damage, most likely by a hydrophobic stacking.
- Published
- 2004
24. (5'S)-8,5'-Cyclo-2'-deoxyguanosine Is a Strong Block to Replication, a Potent pol V-Dependent Mutagenic Lesion, and Is Inefficiently Repaired in Escherichia coli.
- Author
-
Jasti, Vijay P., Das, Rajat S., Hilton, Benjamin A., Weerasooriya, Savithri, Yue Zou,, and Basu, Ashis K.
- Published
- 2011
- Full Text
- View/download PDF
25. Specific and Efficient Binding of Xeroderma Pigmentosum Complementation Group A to Double-Strand/Single-Strand DNA Junctions with 3′- and/or 5′-ssDNA Branches.
- Author
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Zhengguan Yang, Roginskaya, Marina, Co1is, Laureen C., Basu, Ashis K., Shell, Steven M., Yiyong Liu, Musich, Phillip R., Harris, Constance M., Harris, Thomas M., and Yue Zou
- Published
- 2006
- Full Text
- View/download PDF
26. Dimerization of Human XPA and Formation of XPA[sub2]-RPA Protein Complex.
- Author
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Zheng-guan Yang, Yang Liu, Mao, Leslie Y., Jian-Ting Zhang, and Yue Zou
- Published
- 2002
- Full Text
- View/download PDF
27. Intrastrand DNA Cross-Links as Tools for Studying DNA Replication and Repair: Two-, Three-, and Four-Carbon Tethers between the N[sup 2] Positions of Adjacent Guanines.
- Author
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Kowalczyk, Agnieszka, Carmical, J. Russ, Yue Zou, Van Houten, Bennett, Lloyd, R. Stephen, Harris, Constance M., and Harris, Thomas M.
- Published
- 2002
- Full Text
- View/download PDF
28. Hierarchy of DNA Damage Recognition in Escherichia coli Nucleotide Excision Repair.
- Author
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Yue Zou, Luo, Charlie, and Geacintov, Nicholas E.
- Subjects
- *
DNA damage , *ESCHERICHIA coli - Abstract
Examines the hierarchy of DNA damage recognition in nucleotide excision repair in Escherichia coli. Differentiation between initial and second recognition; Role of adenosine triphosphate in DNA damage recognition; Factors influencing the incision efficiency of UvrABC.
- Published
- 2001
- Full Text
- View/download PDF
29. Differential Incision of Bulky Carcinogen--DNA Adducts by the UvrABC Nuclease: Comparison of....
- Author
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Hoare, Sarasija and Yue Zou
- Subjects
- *
DNA-protein interactions , *NUCLEASES , *DNA damage - Abstract
Examines the differential incision of bulky carcinogen-DNA adducts by the UvrABC nuclease. Importance of Escherichia coli UvrABC nuclease system in the removal of DNA damages; Account on UvrABC proteins interaction in DNA lesion sites; Influence of different adducts on UvrA binding affinities; Extent of UvrB-DNA complex formation.
- Published
- 2000
- Full Text
- View/download PDF
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